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Search Results: 1 - 10 of 5201 matches for " Paushali Roy "
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Structural Analysis of Predicted HIV-1 Secis Elements  [PDF]
Paushali Roy, Sayak Ganguli, Pooja Sharma, Protip Basu, Abhijit Datta
World Journal of AIDS (WJA) , 2011, DOI: 10.4236/wja.2011.14030
Abstract: Incorporation of Selenocysteine into protein requires an RNA structural motif, SECIS (Selenocysteine insertion sequence) element that, along with other factors, demarcates UGA-Sec from the UGA termination codon, for expression of Selenoproteins (in case of eukaryotes). It has been predicted that during HIV infection, several functional viral selenoproteins are expressed and synthesis of these viral selenoproteins deplete the selenium level of the host. It might be that even the viral genome has the SECIS elements in their Selenoprotein mRNA, and during infection, the host cellular machinery is transformed in such a way that the human Sec tRNA binds to the viral Selenoprotein mRNA, instead of binding to its own Selenoprotein mRNA, thus leading to expression of viral selenoproteins. This hypothesis was tested in this study by identifying the SECIS elements in the HIV-1 genome and further predicting their secondary and tertiary structures. We then tried to dock these tertiary structures with human Sec tRNA. Here we report putatively the presence of 3215 SECIS elements in the HIV-1 genome and that the human Sec tRNAsec binds to the viral SECIS elements present in the viral selenoprotein mRNA. Based on an earlier finding, it was observed that atoms of A8 and U9, which present in human Sec tRNA, are the possible key sites for binding.
Lysine richness in human snurps – possible sites for electrophilic attacks
Sanjay Kumar Dey,Sayak Ganguli,Abhijit Datta,Paushali Roy
Bioinformation , 2010,
Abstract: Gene-expression strategies are remodeled following exposure to stress. The reactive oxidants and electrophiles generated after stress actually affects the structural and functional properties of different cellular proteins. It is also seen that lysine rich motifs of proteins play crucial role in electrophilic attack and modification. Therefore, this study revealing lysine richness in 5 main human snrups (Small Nuclear Ribonucleoproteins) indicates a possible mechanism of gene regulation under stress. This possibility is highly supported by the findings that surface residues of the molecules were full of lysine rich clusters. Lysine richness is also found to be a highly conserved pattern across the various domains of life indicative of stress adaptation in the prebiotic to biotic world transition. Moreover the modeled structures showed good all atom contacts and minimal outliers.
Structural analysis of Leucocine – an essential bacteriocin
Hirak Jyoti Chakraborty,Sayak Ganguli,Protip Basu,Paushali Roy
International Journal of Bioinformatics Research , 2010,
Abstract: Bacterial peptides of low molecular weight displaying antagonism towards other bacterialmembers are referred to as bacteriocins. Bacteriocins are an essential member of the broadly classifiedgroup of lantibiotics which finds several commercial uses. This work comprises of the determination ofstructure of the most important class of bacteriocins – the leucocin group. Structure elucidation wasperformed using homology modelling approach and the modeled structure was validated using theirRamachandran calculations. Ligand interaction pockets were identified by calculating the Delaunaytriangulation number and structural properties of amino acids were documented. Structure elucidations ofsuch lantibiotics are important for future endeavours towards analyses of protein - protein interactions.
Genome wide snRNP motifs and regulatory sequences in HIV1 isolates
Paushali Roy,Protip Basu,Sayak Ganguli,Abhijit Datta
International Journal of Bioinformatics Research , 2009,
Abstract: The pathogenesis of HIV-1 is complex and characterized by the interplay of both viral and hostfactors. Within HIV 1 genome there are several snRNP motifs responsible for pre mRNA splicing andstabilization. By locating these motifs within the genome and disturbing them may result in an impairedability of the cells to sustain HIV-1 replication. One of such regulatory sequences is riboswitches thatregulate the dimerization of HIV-1 RNA, which is an essential step during packaging. The current workwas undertaken to identify possible regulatory RNA motifs in the HIV1 genome from different isolates.The current work has successfully identified multiple snRNP motifs in the genome sequences ofdifferent strains of HIV-1 isolates. The identification of the multiple snRNP motifs in the genomicsequences of the various isolates lead us to believe that future studies with artificially constructedsnRNPs might have the potential to inhibit HIV1 replication. Apart from containing snRNP motifs theyalso possess regulatory riboswitch motifs. Riboswitches bind metabolites and control the dimerizationand packaging of the genome. Thus the occurrence of such motifs further strengthens the idea thatapart from serving as a regulatory domain for structural constraints such motifs may also regulategenome integration and production of the necessary products by using the host transcriptionalmachinery. It is however beyond doubt that such sequence motifs must have originated in the RNAworld as they have the power to mediate RNA induced regulation of gene expression.
Structural and Functional analysis of glutathione peroxidase from Ricinus communis L.– a computational approach.
Sohini Gupta,Sabuj Saha,Paushali Roy,Protip Basu
International Journal of Bioinformatics Research , 2010,
Abstract: Oxidative stress in plants causes the induction of several enzymes, including superoxidedismutase (EC, ascorbate peroxidase (EC and glutathione reductase (EC Thefirst two are responsible for converting superoxide to H2O2 and its subsequent reduction to H2O, and thethird is involved in recycling of ascorbate. Glutathione peroxidases (GPXs, EC are a family of keyenzymes involved in scavenging oxyradicals in animals. Only recently, indications for the existence of thisenzyme in plants were reported. Genes with significant sequence homology to one member of the animalGPX family, namely phospholipid hydroperoxide glutathione peroxidase (PHGPX), were isolated fromseveral plants. In this paper we report the homology modelling of the glutathione peroxidase protein fromRicinus communis L. and its interactions with its two substrates hydrogen peroxide and glutathione. Specificsites of interaction were identified and ligand binding pockets were also screened.
Retraction: In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase
Sayak Ganguli, Manjita Mazumder, Protip Basu, Paushali Roy, Sayani Mitra, Abhijit Datta
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-258
Phylogenetic signatures of functional conservedness in lantibiotics- an in-silico regulomics study
Protip Basu, Hirak Jyoti Chakraborty, Sayak Ganguli, Paushali Roy, and Abhijit Datta
International Journal of Microbiology Research , 2010,
Abstract: The name Lantibiotics was introduced in 1988 as an abbreviation for "Lanthionine-containingpeptide antibiotics". In spite of this naming, Lantibiotics are not classed as antibiotics. The first structures ofthese antimicrobial agents were produced by pioneering work by Gross and Morell in the late sixties andearly seventies, thus marking the formal introduction of Lantibiotics. Since then Lantibiotics such as Nisinhave been for food preservation and have yet to encounter significant bacterial resistance. These attributesof lantibiotics have led to more detailed research into them
International Journal of Bioinformatics Research , 2011,
Abstract: Snurps or small nuclear ribonucleoproteins (snRNPs), are RNA-protein complexes that combine withunmodified pre-mRNA and various other proteins to form a Spliceosome, comprising of five small nuclear RNAs(snRNAs)—U1, U2, U4, U5, and U6 snRNA—as well as many protein factors, upon which splicing of pre-mRNAoccurs. While, RNA pseudoknots play crucial role in protein synthesis by helping in internal ribosome entry,frameshifting, stop codon readthrough in many viral species and the 3’NCR pseudoknots helps viral RNAs to replicate,has been reported by a number of investigators, its presence in human snurps has not yet been done. The present insilico study reveals the presence of pseudoknots in the mRNAs of the proteins associated with human Spliceosome. Itnot only emphasizes their significance as catalytic RNA world relics but also opens the scope of research in thefunctional and structural associations of RNA pseudoknots in eukaryotic gene regulation.
Probabilistic Prediction for Earthquake in Bangladesh: Just How Big Does the Earthquake Have to Be Next Years?  [PDF]
Shongkour Roy
Open Journal of Earthquake Research (OJER) , 2014, DOI: 10.4236/ojer.2014.32011
Abstract: Earthquakes are more deadly than any other form of natural hazard. Because of this, scientists have been searching for accurate ways to predict earthquakes so that lives can be saved. Statistical analysis is useful methods of predicting earthquakes. They provide additional insights to the seismic hazard. In this work, the statistical analysis has been described through the study of “Region of Bangladesh”. A sample result from the statistical analysis which gives intermediate term prediction of earthquakes is given. At the end of the study, the prediction of near future earth-quakes is also investigated through the pictorial and tabular behaviors.
The “Glocal” Dynamics of Construction Labor and Digital Architecture: Preston Scott Cohen’s Addition to the Tel Aviv Museum as Case Study  [PDF]
Roy Kozlovsky
Journal of Building Construction and Planning Research (JBCPR) , 2015, DOI: 10.4236/jbcpr.2015.32009
Abstract: Globalization and technological change are transforming the ways in which buildings are being designed and built. An overlooked aspect of this development is its impact on construction labor, and the significance of labor for assessing the work of architecture. The paper draws upon the sociological concept of the “glocal” to analyse the construction site as the product of the tension between global and local conditions of architectural production and consumption. The construction of Preston Scott Cohen’s 2010 Tel Aviv Museum Addition serves as its case study for theorizing the “glocal” dynamics of digital architecture, building technology and construction labor. This methodological approach highlights the role of migrant guest workers and technological transfer in contemporary construction culture. To realize with precision the complex design under local constraints, the contractor developed a hybrid work process that interspersed labor saving automated manufacturing techniques with artisanal, skilled construction work. In addition, workers and contractors exercised a high level of control over the pace and method of construction, and devised building solutions which improved upon the architect’s design. In conclusion, the paper argues that construction activity differs from broader trends in manufacturing due to the self-reflexivity of architectural design to its condition of production, but that at the same time, this critical capacity is enabled by the globalization of construction labor.
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